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Cellulose fibres are a sustainable alternative for development of new materials and with chemical modifications the material properties can be tailored for its intended application. To understand the impact of a modification characterisation techniques that reveal where the chemical alterations occur across the fibre are needed. Here we showcase how X-ray spectro-microscopy around the carbon K-edge can provide spatially resolved images of the chemical content of cellulose fibres and investigate the effect of different sample preparation strategies on the resulting data quality. We show that that one can spatially separate different lignin compositions over a single thermomechanical pulp fibre. The sample preparation is key for a successful experiment and requires sectioning of thin slices (~ 100 nm) of the sample which can be achieved by microtome sectioning. The effect of different embedding materials, including epoxies, cryo-embeddings with water and sucrose and elemental sulphur, is evaluated. The results show that epoxy embeddings are beneficial for homogenous sectioning, which is an advantage for imaging, while embedding strategies without carbon species, such as elemental sulphur or cryo-embedding with water, is better for evaluation of the chemical content in the fibre due to less overlap in the spectral signal from the embedding material. We also present measurement strategies for efficient data collection that minimise the inflicted radiation dose to provide guidelines for performing synchrotron-based spectro-microscopy around the carbon K-edge to characterise cellulose fibres.